The foam-forming filamentous bacteria can result in serious membrane fouling problems, not only in traditional activated sludge processes, but also in membrane bioreactors (MBR). In this study, we examine the influence of the hydrophobicity of the membrane on membrane fouling in a submerged MBR using two sets of polytetrafluoroethylene membranes with different surface hydrophobicity We also identify and compare the foam-forming filamentous bacteria via the Eikelboom method, the combination of a polymerase chain reaction with DNA sequencing, and the fluorescent in situ hybridization (FISH) approach based on non-cultured and cultured methods. The experimental results showed that during foaming period, the transmembrame pressure of the high hydrophobicity membrane increased as the flux decreased; but no significant influence was observed for the low hydrophobicity membrane. Of the foam-forming bacteria identified by non-cultured method, only Actinomycetes and Nosotcoida limicola III were observed using Eikelboom identification keys I and II, while high G + C content Gram-positive (HGC) bacteria was the predominant filamentous bacteria identified via the FISH approach. On the other hand, the Microthrix parvicella, Eikelboom type 1851, Eikelboom type 0092, and Flexibacter were identified as the predominant type of filamentous bacteria using the culture method with Eikelboom identification key I. The HGC bacteria made up 77.1% of the total isolates. Finally, the results of 16S rRNA sequences screened by the Eikelboom method showed that the genera Gordonia and Cytophaga, which contributed 75.7% and 20.1%, respectively, were the predominant filamentous bacteria. (c) 2009 Elsevier B.V. All rights reserved.